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AMSEL Report Summary

Project ID: 682144
Funded under: H2020-EU.1.1.

Periodic Reporting for period 1 - AMSEL (Atomic Force Microscopy for Molecular Structure Elucidation)

Reporting period: 2016-06-01 to 2017-11-30

Summary of the context and overall objectives of the project

Molecular structure elucidation is of great importance in synthetic chemistry, pharmacy, life sciences, energy and environmental sciences, and technology applications. To date structure elucidation by atomic force microscopy (AFM) has been demonstrated for a few, small and mainly planar molecules. The applicability of AFM for molecular structure elucidation should be expanded and high-impact scientific questions will be tackled using structure elucidation with the AFM.

A combined low-temperature scanning tunneling microscope/atomic force microscope (LT-STM/AFM) and in situ electrospray deposition method will be developed to expand the applicability of this technique towards larger molecules. Chemical resolution will be improved by novel measurement techniques and by measurements of model compounds building up a database for substructure identification by AFM.

The developed tools and techniques will be applied to molecules of increasing fragility, complexity, size, and three-dimensionality. Samples that are challenging to characterize with conventional methods will be studied. Complex molecular mixtures will be investigated molecule-by-molecule taking advantage of the single-molecule sensitivity. The absolute stereochemistry of molecules will be determined, resolving molecules with multiple stereocenters. The operation of single molecular machines will be investigated. Reactive intermediates generated by atomic manipulation will be characterized and their on-surface reactivity will be studied by AFM. Novel, custom designed molecules will be created by atomic manipulation.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

AFM for molecular structure determination was applied to the characterization of complex molecular mixtures and the characterization of molecules formed by atom manipulation and the characterization of model compounds.

Several hundred individual molecules were resolved in heavy oil based mixtures of different origin and different processing steps applied obtaining information on molecular geometry, aromaticity, types and locations of heterocycles, occurrence, length and connectivity of alkyl chains, and content of archipelago-type architectures.
Schuler, B.; Fatayer, S.; Meyer, G.; Rogel, E.; Moir, M.; Zhang, Y.; Harper, M. R.; Pomerantz, A. E.; Bake, K. D.; Witt, M.; Peña, D.; Kushnerick J. Douglas; Mullins, O. C.; Ovalles, C.; van den Berg, F. G. A. & Gross, L. “Heavy oil based mixtures of different origins and treatments studied by AFM” Energy & Fuels 31, 6856–6861 (2017).

Triangulene, an elusive molecule with a high spin ground state was generated by atom manipulation and its open-shell character was revealed by scanning tunnelling microscopy.
Pavliček, N.; Mistry, A.; Majzik, Z.; Moll, N.; Meyer, G.; Fox, D. J.; Gross, L.; “Synthesis and characterization of triangulene” Nature Nanotechnology 12, 308–311 (2017), journal cover.

Meta-arynes have been created by atom manipulation. The manipulation process was investigated for different surfaces. The diradical structure of the meta-aryne was confirmed and characterized by AFM on ultrathin NaCl films.
Pavliček, N.; Majzik, Z.; Collazos, S.; Meyer, G.; Pérez, D.; Guitian, E.; Peña, D. & Gross, L. “Generation and Characterization of a Meta-Aryne on Cu and NaCl Surfaces”, ACS Nano, 11, 10768–10773 (2017).

Molecules with aliphatic moieties, including alkyl and alkenyl chains were measured increasing the number of model compounds for substructure identification by AFM. The chirality of a molecule was determined by AFM and switched by atom manipulation
Schuler, B.; Zhang, Y.; Collazos, S.; Fatayer, S.; Meyer, G.; Pérez, D.; Guitián, E.; Harper, M. R.; Kushnerick, J. D.; Peña, D.; Gross, L.; “Characterizing aliphatic moieties in hydrocarbons with atomic force microscopy” Chem. Sci. 8, 2315-232 (2017).

A review about molecular structure elucidation and atom manipulation with AFM was written.
Pavliček, N.; Gross, L.; “Generation, manipulation and characterization of molecules by atomic force microscopy” Nat. Rev. Chem. 1, 0005 (2017)

A combined low temperature scanning tunnelling microscope/atomic force microscope (LT-STM/AFM) with an electrospray ionization (ESI) is being set up. The LT-STM/AFM is fully operational, the ESI is under construction.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

The applicability, throughput, and resolution of AFM for molecular structure elucidation will be increased to solve high-impact scientific questions and debates regarding molecular structures in the fields of chemistry, pharmacy, energy, ecology, synthesis, life science, and molecular electronics.

Resolution, in particular chemical sensitivity, will benefit from novel measurement techniques, improved theory, and the build-up on an open database for molecular structure identification by AFM. We will set up a new tool combing atomic force microscopy electrospray ionization deposition significantly expanding the classes of molecules that can be studied with atomic resolution AFM.

High impact results can be expected on molecules that will include large, non-planar, and chiral molecules, reaction products, reactive intermediates and radicals created by atomic manipulation, molecular machines, and complex molecular mixtures, e.g. mixtures found in nature, fuel residues, combustion products or petrol heavy fractions.
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